Peanut (Arachis hypogaea) is a segmental allotetraploid oilseed legume (AABB; 2n = 4x = 40), with a genome size of 2.7Gb that arose from the hybridization of Arachis duranensis and Arachis ipaensis. It is an important crop that is grown in more than 100 countries. It is rich in nutrients such as proteins, carbohydrates, vitamins and other micro-nutrients. It also contains phytochemicals such as folates, flavonoids, tocopherols and trans-resveratrol that are significant in human nutrition. The process of tetraploidization and domestication contributed to the reduction of genetic polymorphism in the crop. Since the cultivated and wild peanut differ in ploidy, it is not easy to use the secondary germplasm pool for peanut improvement. To address this challenge, a chromosome segment substitution line (CSSL) population was developed as a way of incorporating alleles from the wild species into cultivated peanut. In the course of this study, the CSSL population was genotyped with high-density SNP markers. The SNPs facilitated a clearer delineation of the wild derived introgressions, in addition to highlighting tetrasomic recombination events. Further investigations explored the contributions of the introgressions to phenotype. It was clear that the introgressions had introduced novel variations into the cultivated background. These included changes in vegetative and reproductive habits, alteration of seed composition traits, improvement in agronomically important attributes such as pod weight, pod yield and variation in disease resistance. In addition to obtaining phenotype data by the conventional manual means, this study explored the possibility of deploying field-based high-throughput phenotyping techniques to study peanut. The utility of spectral indices as selection tools was demonstrated. Nondestructive below ground phenotyping of pod yield was done using ground penetrating radar. Though still nascent, the technology has the potential to revolutionize the peanut breeding pipeline.